So I downgraded to 2.011 and tried the discovery and all the devices were present. Reinstalled 3.09 and also 3.07 and only two devices were discovered. I just downgraded to 2.011 again and it is working

I tried stopping indigo completely, disabling and enabling the plugin as well as downgrading and upgrading. As you say it looks like the devices are published but they don't show up in Alexa (well only 2 of 53 do)

I have just run a test on my test system and it is working as I expected.

I deleted all my Alexa-Hue Bridge devices.

Installed 2.0.11

Added 3 Alexa-Hue bridges with two devices each

Ran discovery - 6 devices found

Deleted Alexa devices using iOS App

Upgraded to 3.0.9

Edited and saved each of the Alexa-Hue bridges in turn. Each converted two devices.

Ran discovery - 6 devices found

I am wondering whether it is something to do with the number of devices because you have 25 on Alexa-Hue Bridge 1 and 27 on Alexa Hue Bridge 2. As you say it works OK in 2.0.11 so this is a bit of a mystery at the moment.

If you feel inclined, it might be worth trying:

Delete Alexa devices using iOS App

Install 3.0.9

Edit and save each of the Alexa-Hue bridges in turn thereby converting devices.

It looks like there is some sort of buffer limit being exceeded. I can't discover any devices on an Alexa-Hue bridge that has 25 or more devices - 24 or under work OK.

I suspect the reason might be that the unique ID that Alexa uses to request the plugin to turn on/off or dim a device is a 64 character string. Previously it was a short Indigo device Id. This seems to have tipped it over the edge - the V2 limit was 27 devices.

I think I am going to place a limit of 20 devices per Alexa-Hue Bridge to be on the safe side. This isn't really a problem given that one can define multiple Alexa-Hue bridges.

The work-around for you is to reduce the number of devices on each existing Alexa-Hue bridge to < 25 (in my testing) by moving the excess devices to Alexa-Hue bridge 3.So just install V3 as before and then edit and save all the Alexa-Hue bridge devices to make sure the conversion from V2 is saved. Then go back and select devices to delete from Alexa-Hue Bridges 1 & 2 and then add them to Alexa-Hue Bridge 3.